libSBML Python API
5.10.0
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{comp}
comp Implementation of the “comp” package extention to the Model construct.The CompModelPlugin class inherits from the SBMLSBasePlugin class, and codifies the extentions to the Model class defined in the SBML Level 3 Hierarchical Model Composition package (“comp”). This extention allows a Model to define Submodels (other Models that are instantiated as new parts of the parent Model), and Ports, a defined interface for including the given Model as a Submodel of a different Model.
Submodels are stored in an optional child ListOfSubmodels object, which, if present, must contain one or more Submodel objects. All of the Submodels present in the ListOfSubmodels are defined to be instantiated in the 'complete' Model.
Ports are stored in an optional child ListOfPorts object, which, if present, must contain one or more Port objects. All of the Ports present in the ListOfPorts collectively define the 'port interface' of the Model.
Public Member Functions | |
def | addPort |
def | addReplacedElement |
def | addSubmodel |
def | clearReplacedElements |
def | clone |
def | createPort |
def | createReplacedBy |
def | createReplacedElement |
def | createSubmodel |
def | getDivider |
def | getElementByMetaId |
def | getElementBySId |
def | getElementNamespace |
def | getLevel |
def | getListOfAllElements |
def | getListOfPorts |
def | getListOfReplacedElements |
def | getListOfSubmodels |
def | getNumPorts |
def | getNumReplacedElements |
def | getNumSubmodels |
def | getPackageName |
def | getPackageVersion |
def | getParentSBMLObject |
def | getPort |
def | getPrefix |
def | getReplacedBy |
def | getReplacedElement |
def | getSBMLDocument |
def | getSubmodel |
def | getTransformer |
def | getURI |
def | getVersion |
def | isSetReplacedBy |
def | isSetTransformer |
def | logInvalidId |
def | removePort |
def | removeReplacedElement |
def | removeSubmodel |
def | setDivider |
def | setElementNamespace |
def | setReplacedBy |
def | setTransformer |
def | unsetReplacedBy |
def | unsetTransformer |
def libsbml.CompModelPlugin.addPort | ( | self, | |
args | |||
) |
Python method signature(s):
addPort(CompModelPlugin self, Port port)int
Adds a copy of the given Port object to the list of ports.
port | the Port object to be added to the list of ports. Fails if the added port is None , does not match the level/version/package of the parent object, or cannot be added to the list of ports. |
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inherited |
Python method signature(s):
addReplacedElement(CompSBasePlugin self, ReplacedElement replacedElement)int
Adds a copy of the given ReplacedElement object to the list of ReplacedElements.
replacedElement | the ReplacedElement object to be added to the list of ReplacedElements. Fails if the added ReplacedElement is None , does not match the level/version/package of the parent object, or cannot be added to the list of replaced elements. |
def libsbml.CompModelPlugin.addSubmodel | ( | self, | |
args | |||
) |
Python method signature(s):
addSubmodel(CompModelPlugin self, Submodel submodel)int
Adds a copy of the given Submodel object to the list of submodels.
Fails if the added submodel is None
, does not match the level/version/package of the parent object, or cannot be added to the list of submodels.
submodel | the Submodel object to be added to the list of submodels. |
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inherited |
Python method signature(s):
clearReplacedElements(CompSBasePlugin self)
Remove all ReplacedElements, if any exist.
def libsbml.CompModelPlugin.clone | ( | self | ) |
{comp}
comp Implementation of the “comp” package extention to the Model construct.The CompModelPlugin class inherits from the SBMLSBasePlugin class, and codifies the extentions to the Model class defined in the SBML Level 3 Hierarchical Model Composition package (“comp”). This extention allows a Model to define Submodels (other Models that are instantiated as new parts of the parent Model), and Ports, a defined interface for including the given Model as a Submodel of a different Model.
Submodels are stored in an optional child ListOfSubmodels object, which, if present, must contain one or more Submodel objects. All of the Submodels present in the ListOfSubmodels are defined to be instantiated in the 'complete' Model.
Ports are stored in an optional child ListOfPorts object, which, if present, must contain one or more Port objects. All of the Ports present in the ListOfPorts collectively define the 'port interface' of the Model. Python method signature(s):
clone(CompModelPlugin self)CompModelPlugin
Creates and returns a deep copy of this CompModelPlugin object.
def libsbml.CompModelPlugin.createPort | ( | self | ) |
Python method signature(s):
createPort(CompModelPlugin self)Port
Creates a Port object, adds it to the end of the port objects list and returns a pointer to the newly created object.
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inherited |
Python method signature(s):
createReplacedBy(CompSBasePlugin self)ReplacedBy
Creates a new, empty ReplacedBy, adds it to this CompSBasePlugin and returns the created ReplacedBy.
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inherited |
Python method signature(s):
createReplacedElement(CompSBasePlugin self)ReplacedElement
Creates a ReplacedElement object, adds it to the end of the ReplacedElement objects list and returns a pointer to the newly created object.
def libsbml.CompModelPlugin.createSubmodel | ( | self | ) |
Python method signature(s):
createSubmodel(CompModelPlugin self)Submodel
Creates a Submodel object, adds it to the end of the submodel objects list and returns a pointer to the newly created object.
def libsbml.CompModelPlugin.getDivider | ( | self | ) |
Python method signature(s):
getDivider(CompModelPlugin self)string
Get the string used as the divider between names when renaming and flattening models.
The divider string consists of two underscore characters ("<code>__</code>") by default, and can be overridden with the setDivider() function.
def libsbml.CompModelPlugin.getElementByMetaId | ( | self, | |
args | |||
) |
Python method signature(s):
getElementByMetaId(CompModelPlugin self, string metaid)SBase
Returns the first child element it can find with the given meta identifier, or itself if it has the given metaid
, or None
if no such object is found.
metaid | a string representing the metaid of objects to find. |
metaid
. def libsbml.CompModelPlugin.getElementBySId | ( | self, | |
args | |||
) |
Python method signature(s):
getElementBySId(CompModelPlugin self, string id)SBase
Returns the first child element found that has the given id
in the model-wide SId namespace, or None
if no such object is found.
id | a string representing the id of objects to find. |
id
.
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inherited |
{core}
Representation of a plug-in object of SBML's package extension.Additional attributes and/or elements of a package extension which are directly contained by some pre-defined element are contained/accessed by SBasePlugin class which is extended by package developers for each extension point. The extension point, which represents an element to be extended, is identified by a combination of a Package name and a typecode of the element, and is represented by SBaseExtensionPoint class.
For example, the layout extension defines <listOfLayouts> element which is directly contained in <model> element of the core package. In the layout package (provided as one of example packages in libSBML-5), the additional element for the model element is implemented as ListOfLayouts class (an SBase derived class) and the object is contained/accessed by a LayoutModelPlugin class (an SBasePlugin derived class).
SBasePlugin class defines basic virtual functions for reading/writing/checking additional attributes and/or top-level elements which should or must be overridden by subclasses like SBase class and its derived classes.
Package developers must implement an SBasePlugin exntended class for each element to be extended (e.g. SBMLDocument, Model, ...) in which additional attributes and/or top-level elements of the package extension are directly contained.
To implement reading/writing functions for attributes and/or top-level elements of the SBsaePlugin extended class, package developers should or must override the corresponding virtual functions below provided in the SBasePlugin class:
reading elements :
virtual SBase createObject (XMLInputStream stream)
This function must be overridden if one or more additional elements are defined.
virtual bool readOtherXML (SBase parentObject, XMLInputStream stream)
This function should be overridden if elements of annotation, notes, MathML, etc. need to be directly parsed from the given XMLInputStream object.
reading attributes (must be overridden if additional attributes are defined) :
virtual void addExpectedAttributes(ExpectedAttributes& attributes)
virtual void readAttributes (XMLAttributes attributes, ExpectedAttributes& expectedAttributes)
writing elements (must be overridden if additional elements are defined) :
virtual void writeElements (XMLOutputStream stream)
writing attributes :
virtual void writeAttributes (XMLOutputStream stream)
This function must be overridden if one or more additional attributes are defined.
virtual void writeXMLNS (XMLOutputStream stream)
This function must be overridden if one or more additional xmlns attributes are defined.
checking elements (should be overridden) :
virtual bool hasRequiredElements()
checking attributes (should be overridden) :
virtual bool hasRequiredAttributes()
To implement package-specific creating/getting/manipulating functions of the SBasePlugin derived class (e.g., getListOfLayouts(), createLyout(), getLayout(), and etc are implemented in LayoutModelPlugin class of the layout package), package developers must newly implement such functions (as they like) in the derived class.
SBasePlugin class defines other virtual functions of internal implementations such as:
virtual void setSBMLDocument(SBMLDocument d)
virtual void connectToParent(SBasesbase)
virtual void enablePackageInternal(string pkgURI, string pkgPrefix, bool flag)
These functions must be overridden by subclasses in which one or more top-level elements are defined.
For example, the following three SBasePlugin extended classes are implemented in the layout extension:
SBMLDocumentPlugin class for SBMLDocument element
(SBMLDocumentPlugin class is a common SBasePlugin extended class for SBMLDocument class. Package developers can use this class as-is if no additional elements/attributes (except for required attribute) is needed for the SBMLDocument class in their packages, otherwise package developers must implement a new SBMLDocumentPlugin derived class.)
LayoutModelPlugin class for Model element
<listOfLayouts> element is added to Model object.
The following virtual functions for reading/writing/checking are overridden: (type of arguments and return values are omitted)
createObject()
: (read elements) readOtherXML()
: (read elements in annotation of SBML L2) writeElements()
: (write elements) The following virtual functions of internal implementations are overridden: (type of arguments and return values are omitted)
setSBMLDocument()
connectToParent()
enablePackageInternal()
The following creating/getting/manipulating functions are newly implemented: (type of arguments and return values are omitted)
getListOfLayouts()
getLayout ()
addLayout()
createLayout()
removeLayout()
getNumLayouts()
LayoutSpeciesReferencePlugin class for SpeciesReference element (used only for SBML L2V1)
id attribute is internally added to SpeciesReference object only for SBML L2V1
The following virtual functions for reading/writing/checking are overridden: (type of arguments and return values are omitted)
readOtherXML()
writeAttributes()
Python method signature(s):
getElementNamespace(SBasePlugin self)string
Returns the XML namespace (URI) of the package extension of this plugin object.
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inherited |
Python method signature(s):
getLevel(SBasePlugin self)long
Returns the SBML level of the package extension of this plugin object.
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inherited |
def libsbml.CompModelPlugin.getListOfPorts | ( | self | ) |
Python method signature(s):
getListOfPorts(CompModelPlugin self)ListOfPorts
Returns the ListOf object that holds all ports.
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inherited |
Python method signature(s):
getListOfReplacedElements(CompSBasePlugin self)ListOfReplacedElements
Returns the ListOf object that holds all replacedElements.
def libsbml.CompModelPlugin.getListOfSubmodels | ( | self | ) |
Python method signature(s):
getListOfSubmodels(CompModelPlugin self)ListOfSubmodels
Returns the ListOf object that holds all submodels.
def libsbml.CompModelPlugin.getNumPorts | ( | self | ) |
Python method signature(s):
getNumPorts(CompModelPlugin self)long
Returns the number of ports for this CompModelPlugin.
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inherited |
Python method signature(s):
getNumReplacedElements(CompSBasePlugin self)long
Returns the number of ReplacedElements for this CompSBasePlugin.
def libsbml.CompModelPlugin.getNumSubmodels | ( | self | ) |
Python method signature(s):
getNumSubmodels(CompModelPlugin self)long
Returns the number of submodels for this CompModelPlugin.
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inherited |
Python method signature(s):
getPackageName(SBasePlugin self)string
Returns the package name of this plugin object.
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inherited |
Python method signature(s):
getPackageVersion(SBasePlugin self)long
Returns the package version of the package extension of this plugin object.
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inherited |
Python method signature(s):
getParentSBMLObject(SBasePlugin self)SBase getParentSBMLObject(SBasePlugin self)
SBase
Returns the parent SBase object to which this plugin object connected.
def libsbml.CompModelPlugin.getPort | ( | self, | |
args | |||
) |
Python method signature(s):
getPort(CompModelPlugin self, long n)Port getPort(CompModelPlugin self, long n)
Port getPort(CompModelPlugin self, string id)
Port getPort(CompModelPlugin self, string id)
Port
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
getPort(string id)
Returns the port with the given identifier.
id | the id of the Port to get. |
None
is returned.getPort(long n)
Returns the port with the given index.
n | the index number of the Port to get. |
n
is invalid, None
is returned.
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inherited |
Python method signature(s):
getPrefix(SBasePlugin self)string
Returns the prefix of the package extension of this plugin object.
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inherited |
Python method signature(s):
getReplacedBy(CompSBasePlugin self)ReplacedBy getReplacedBy(CompSBasePlugin self)
ReplacedBy
Get the child ReplacedBy of this SBase.
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inherited |
Python method signature(s):
getReplacedElement(CompSBasePlugin self, long n)ReplacedElement getReplacedElement(CompSBasePlugin self, long n)
ReplacedElement
Returns the ReplacedElement with the given index.
n | the index number of the ReplacedElement to get. |
None
is returned.
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inherited |
Python method signature(s):
getSBMLDocument(SBasePlugin self)SBMLDocument getSBMLDocument(SBasePlugin self)
SBMLDocument
Returns the parent SBMLDocument of this plugin object.
def libsbml.CompModelPlugin.getSubmodel | ( | self, | |
args | |||
) |
Python method signature(s):
getSubmodel(CompModelPlugin self, long n)Submodel getSubmodel(CompModelPlugin self, long n)
Submodel getSubmodel(CompModelPlugin self, string id)
Submodel getSubmodel(CompModelPlugin self, string id)
Submodel
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
getSubmodel(string id)
Returns the submodel with the given identifier.
id | the identifier of the Submodel to get. |
id
exists, None
is returned.getSubmodel(long n)
Returns the submodel with the given index.
n | the index number of the Submodel to get. |
n
is invalid, None
is returned. def libsbml.CompModelPlugin.getTransformer | ( | self | ) |
Python method signature(s):
getTransformer(CompModelPlugin self)PrefixTransformer *
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inherited |
Python method signature(s):
getURI(SBasePlugin self)string
Gets the URI to which this element belongs to. For example, all elements that belong to SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/core'; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/layout/version1/'
Unlike getElementNamespace, this function first returns the URI for this element by looking into the SBMLNamespaces object of the document with the its package name. if not found it will return the result of getElementNamespace
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inherited |
Python method signature(s):
getVersion(SBasePlugin self)long
Returns the SBML version of the package extension of this plugin object.
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inherited |
Python method signature(s):
isSetReplacedBy(CompSBasePlugin self)bool
Predicate for testing whether the ReplacedBy for this SBase is set.
True
if the ReplacedBy of this SBase is set, False
otherwise. def libsbml.CompModelPlugin.isSetTransformer | ( | self | ) |
Python method signature(s):
isSetTransformer(CompModelPlugin self)bool
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inherited |
Python method signature(s):
logInvalidId(CompSBasePlugin self, string attribute, string wrongattribute)
Helper to log a common type of error.
def libsbml.CompModelPlugin.removePort | ( | self, | |
args | |||
) |
Python method signature(s):
removePort(CompModelPlugin self, long index)Port
Removes the port with the given index.
index | the index of the Port object to remove |
None
is returned if the given index is out of range.
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inherited |
Python method signature(s):
removeReplacedElement(CompSBasePlugin self, long index)ReplacedElement
Removes the ReplacedElement with the given index.
A pointer to the ReplacedElement that was removed is returned. If no ReplacedElement has been removed, None
is returned.
index | the index of the ReplacedElement object to remove |
None
is returned if the given index is out of range. def libsbml.CompModelPlugin.removeSubmodel | ( | self, | |
args | |||
) |
Python method signature(s):
removeSubmodel(CompModelPlugin self, long index)Submodel
Removes the submodel with the given index. A pointer to the submodel that was removed is returned.
index | the index of the Submodel object to remove |
None
is returned if the given index
is out of range and no submodel has been removed, None
is returned. def libsbml.CompModelPlugin.setDivider | ( | self, | |
args | |||
) |
Python method signature(s):
setDivider(CompModelPlugin self, string divider)int
Set the string used as the divider between names when renaming and flattening models.
The divider string consists of two underscore characters ("<code>__</code>") by default. This method will fail if called with an empty divider
, or a divider
that cannot be used internally as part of a valid SBML SId.
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inherited |
Python method signature(s):
setElementNamespace(SBasePlugin self, string uri)int
Sets the XML namespace to which this element belongs to. For example, all elements that belong to SBML Level 3 Version 1 Core must set the namespace to 'http://www.sbml.org/sbml/level3/version1/core'; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must set the namespace to 'http://www.sbml.org/sbml/level3/version1/layout/version1/'
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inherited |
Python method signature(s):
setReplacedBy(CompSBasePlugin self, ReplacedBy replacedBy)int
Sets the ReplacedBy definition of this SBase to a copy of the given ReplacedBy object instance.
This method fails if the added ReplacedBy does not match the level/version/package of the parent object or if the added ReplacedBy cannot be copied.
replacedBy | the ReplacedBy object instance to use. |
def libsbml.CompModelPlugin.setTransformer | ( | self, | |
args | |||
) |
Python method signature(s):
setTransformer(CompModelPlugin self, PrefixTransformer * transformer)
Sets the custom transformer that is to be used, instead of the standard prefixing with the given divider. This makes it possible to finely control how elements are altered.
If not set, only ids and meta ids will be prefixed.
NOTE: the model plugin only holds the pointer to the element it does not take ownership of it. Thus the calling program is responsible of freeing the transformer when no longer needed (i.e after the SBML document has been deleted)
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inherited |
Python method signature(s):
unsetReplacedBy(CompSBasePlugin self)int
Unsets the child ReplacedBy of this SBase.
def libsbml.CompModelPlugin.unsetTransformer | ( | self | ) |
Python method signature(s):
unsetTransformer(CompModelPlugin self)
Unsets any custom prefix transformers.